Hi,
we are running distinct instances on 80 and 8080 -
when you use the 8080 instance - the url is built for /galaxy not
:8080/galaxy
http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=http%3A//genome.ein
stein.yu.edu/galaxy/tool_runner&tool_id=ucs
thus you cannot pass the data back to the correct instance.
What/where is the easiest to pass the 8080 information to the browser?
Looking at some candidate files:
ucsc_proxy.py
ucsc_tablebrowser.xml
but perhaps there is a better way,
best,
joe

I am aware that this is an old question, but I am experiencing exactly the same issue: Galaxy is running on http://address:8080/galaxy, but outputs from "Get Data" tools are sent to http://address/galaxy/tool_runner, which obviously does not exist. Note that it does not only happen with UCSC, but with any other external source of data.

I have been carefully reviewing that NGINX.conf and the Galaxy.ini files, to no avail. Any ideas? Thanks a lot!

Hi! I originally published a message on this thread explaining that I had come across the same obstacle - upon realizing that it was wrongly posted as an answer, I moved it to the comments section.

Instead, I am now sharing what I did to solve the problem, which I hope can be of use for any Galaxy user that happens to bump into the same. Namely, you only need to open your NGINX configuration file (probably in /etc/nginx/nginx.conf) and there make some changes to your server block.

I simply changed X-Forwarded-Host $host to X-Forwarded-Host $host:8080 and it started to work fine. I have not tested it thoroughly, but to my understanding now external tools should be aware of the exact URL they should generate.